I have cleaned, bleached, scrubbed under the bowl and nothing will make the smell go away. I have read that some toilets are not glazed under the rim and can absorb smelly stuff. The smell comes from the bowl if you get down and smell it. There is no smell from the base if you get down close to the floor with your nose. If the problem was the wax ring would it smell from the bowl?

Did you empty the tank and pour 1/2 gallon of bleach down past the flapper and around the rim to get rid of any bad smells that may be lurking down there? Let me know if it helps. Good luck, Tom